Love these ideas so much, but you are trying to do a lot with this game that I don't like.

I honestly feel like this would be a whole lot better with just the region, characters and plotline and leaving out a lot of arbitrary features [that are a. overused and b. not easy to fully implement] like shadow Pokemon and exploring all the regions.

In all honesty though I really love what you have here, I hope you can turn this into a nice game one day